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Visible and Ultraviolet Spectroscopy

1. Background

An obvious difference between certain compounds is their color. Thus, quinone is yellow; chlorophyll is green; the 2,4-dinitrophenylhydrazone derivatives of aldehydes and ketones range in color from bright yellow to deep red, depending on double bond conjugation; and aspirin is colorless. In this respect the human eye is functioning as a spectrometer analyzing the light reflected from the surface of a solid or passing through a liquid. Although we see sunlight (or white light) as uniform or homogeneous in color, it is actually composed of a broad range of radiation wavelengths in the ultraviolet (UV), visible and infrared (IR) portions of the spectrum. As shown on the right, the component colors of the visible portion can be separated by passing sunlight through a prism, which acts to bend the light in differing degrees according to wavelength. Electromagnetic radiation such as visible light is commonly treated as a wave phenomenon, characterized by a wavelength or frequency. Wavelength is defined on the left below, as the distance between adjacent peaks (or troughs), and may be designated in meters, centimeters or nanometers (10^-9 meters). Frequency is the number of wave cycles that travel past a fixed point per unit of time, and is usually given in cycles per second, or hertz (Hz). Visible wavelengths cover a range from approximately 400 to 800 nm. The longest visible wavelength is red and the shortest is violet. Other common colors of the spectrum, in order of decreasing wavelength, may be remembered by the mnemonic: ROY G BIV. The wavelengths of what we perceive as particular colors in the visible portion of the spectrum are displayed and listed below. In horizontal diagrams, such as the one on the bottom left, wavelength will increase on moving from left to right. 

	Violet:   400 - 420 nm  Indigo:   420 - 440 nm  Blue:   440 - 490 nm  Green:   490 - 570 nm  Yellow:   570 - 585 nm  Orange:   585 - 620 nm  Red:   620 - 780 nm

When white light passes through or is reflected by a colored substance, a characteristic portion of the mixed wavelengths is absorbed. The remaining light will then assume the complementary color to the wavelength(s) absorbed. This relationship is demonstrated by the color wheel shown on the right. Here, complementary colors are diametrically opposite each other. Thus, absorption of 420-430 nm light renders a substance yellow, and absorption of 500-520 nm light makes it red. Green is unique in that it can be created by absoption close to 400 nm as well as absorption near 800 nm.
Early humans valued colored pigments, and used them for decorative purposes. Many of these were inorganic minerals, but several important organic dyes were also known. These included the crimson pigment, kermesic acid, the blue dye, indigo, and the yellow saffron pigment, crocetin. A rare dibromo-indigo derivative, punicin, was used to color the robes of the royal and wealthy. The deep orange hydrocarbon carotene is widely distributed in plants, but is not sufficiently stable to be used as permanent pigment, other than for food coloring. A common feature of all these colored compounds, displayed below, is a system of extensively conjugated pi-electrons.

2. The Electromagnetic Spectrum

The visible spectrum constitutes but a small part of the total radiation spectrum. Most of the radiation that surrounds us cannot be seen, but can be detected by dedicated sensing instruments. Thiselectromagnetic spectrum ranges from very short wavelengths (including gamma and x-rays) to very long wavelengths (including microwaves and broadcast radio waves). The following chart displays many of the important regions of this spectrum, and demonstrates the inverse relationship between wavelength and frequency (shown in the top equation below the chart).

The energy associated with a given segment of the spectrum is proportional to its frequency. The bottom equation describes this relationship, which provides the energy carried by a photon of a given wavelength of radiation.

3. UV-Visible Absorption Spectra

To understand why some compounds are colored and others are not, and to determine the relationship of conjugation to color, we must make accurate measurements of light absorption at different wavelengths in and near the visible part of the spectrum. Commercial optical spectrometers enable such experiments to be conducted with ease, and usually survey both the near ultraviolet and visible portions of the spectrum.

The visible region of the spectrum comprises photon energies of 36 to 72 kcal/mole, and the near ultraviolet region, out to 200 nm, extends this energy range to 143 kcal/mole. Ultraviolet radiation having wavelengths less than 200 nm is difficult to handle, and is seldom used as a routine tool for structural analysis.

The energies noted above are sufficient to promote or excite a molecular electron to a higher energy orbital. Consequently, absorption spectroscopy carried out in this region is sometimes called "electronic spectroscopy". A diagram showing the various kinds of electronic excitation that may occur in organic molecules is shown on the left. Of the six transitions outlined, only the two lowest energy ones (left-most, colored blue) are achieved by the energies available in the 200 to 800 nm spectrum. As a rule, energetically favored electron promotion will be from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO), and the resulting species is called an excited state.
When sample molecules are exposed to light having an energy that matches a possible electronic transition within the molecule, some of the light energy will be absorbed as the electron is promoted to a higher energy orbital. An optical spectrometer records the wavelengths at which absorption occurs, together with the degree of absorption at each wavelength. The resulting spectrum is presented as a graph of absorbance (A) versus wavelength, as in the isoprene spectrum shown below. Since isoprene is colorless, it does not absorb in the visible part of the spectrum and this region is not displayed on the graph. Absorbance usually ranges from 0 (no absorption) to 2 (99% absorption), and is precisely defined in context with spectrometer operation.

Because the absorbance of a sample will be proportional to the number of absorbing molecules in the spectrometer light beam (e.g. their molar concentration in the sample tube), it is necessary to correct the absorbance value for this and other operational factors if the spectra of different compounds are to be compared in a meaningful way. The corrected absorption value is called "molar absorptivity", and is particularly useful when comparing the spectra of different compounds and determining the relative strength of light absorbing functions (chromophores). Molar absorptivity (ε) is defined as:

Molar Absorptivity, ε = A / c l

(where A= absorbance, c = sample concentration in moles/liter & l = length of light path through the sample in cm.)
If the isoprene spectrum on the right was obtained from a dilute hexane solution (c = 4 * 10^-5 moles per liter) in a 1 cm sample cuvette, a simple calculation using the above formula indicates a molar absorptivity of 20,000 at the maximum absorption wavelength. Indeed the entire vertical absorbance scale may be changed to a molar absorptivity scale once this information about the sample is in hand. Clicking on the spectrum will display this change in units.

Chromophore Example Excitation λmax, nm ε Solvent C=C Ethene π  __>   π* 171 15,000 hexane C≡C 1-Hexyne π  __>   π* 180 10,000 hexane C=O Ethanal n  __>  π* π  __>  π* 290 180 15 10,000 hexane hexane N=O Nitromethane n  __>  π* π  __>  π* 275 200 17 5,000 ethanol ethanol C-X   X=Br       X=I Methyl bromide Methyl Iodide n  __>  σ* n  __>  σ* 205 255 200 360 hexane hexane

From the chart above it should be clear that the only molecular moieties likely to absorb light in the 200 to 800 nm region are pi-electron functions and hetero atoms having non-bonding valence-shell electron pairs. Such light absorbing groups are referred to as chromophores. A list of some simple chromophores and their light absorption characteristics is provided on the left above. The oxygen non-bonding electrons in alcohols and ethers do not give rise to absorption above 160 nm. Consequently, pure alcohol and ether solvents may be used for spectroscopic studies.
The presence of chromophores in a molecule is best documented by UV-Visible spectroscopy, but the failure of most instruments to provide absorption data for wavelengths below 200 nm makes the detection of isolated chromophores problematic. Fortunately, conjugation generally moves the absorption maxima to longer wavelengths, as in the case of isoprene, so conjugation becomes the major structural feature identified by this technique.
Molar absorptivities may be very large for strongly absorbing chromophores (>10,000) and very small if absorption is weak (10 to 100). The magnitude ofε reflects both the size of the chromophore and the probability that light of a given wavelength will be absorbed when it strikes the chromophore.

4. The Importance of Conjugation 

A comparison of the absorption spectrum of 1-pentene, λ_max = 178 nm, with that of isoprene (above) clearly demonstrates the importance of chromophore conjugation. Further evidence of this effect is shown below. The spectrum on the left illustrates that conjugation of double and triple bonds also shifts the absorption maximum to longer wavelengths. From the polyene spectra displayed in the center diagram, it is clear that each additional double bond in the conjugated pi-electron system shifts the absorption maximum about 30 nm in the same direction. Also, the molar absorptivity (ε) roughly doubles with each new conjugated double bond. Spectroscopists use the terms defined in the table on the right when describing shifts in absorption. Thus, extending conjugation generally results in bathochromic and hyperchromic shifts in absorption.
The appearance of several absorption peaks or shoulders for a given chromophore is common for highly conjugated systems, and is often solvent dependent. This fine structure reflects not only the different conformations such systems may assume, but also electronic transitions between the different vibrational energy levels possible for each electronic state. Vibrational fine structure of this kind is most pronounced in vapor phase spectra, and is increasingly broadened and obscured in solution as the solvent is changed from hexane to methanol.

To understand why conjugation should cause bathochromic shifts in the absorption maxima of chromophores, we need to look at the relative energy levels of the pi-orbitals. When two double bonds are conjugated, the four p-atomic orbitals combine to generate four pi-molecular orbitals (two are bonding and two are antibonding). This was described earlier in the section concerning diene chemistry. In a similar manner, the three double bonds of a conjugated triene create six pi-molecular orbitals, half bonding and half antibonding. The energetically most favorable π  ^__> π* excitation occurs from the highest energy bonding pi-orbital (HOMO) to the lowest energy antibonding pi-orbital (LUMO).
The following diagram illustrates this excitation for an isolated double bond (only two pi-orbitals) and, for a conjugated diene and triene. In each case the HOMO is colored blue and the LUMO is colored magenta. Increased conjugation brings the HOMO and LUMO orbitals closer together. The energy (ΔE) required to effect the electron promotion is therefore less, and the wavelength that provides this energy is increased correspondingly (remember   λ = h • c/ΔE ).

Examples of π __> π* Excitation

Many other kinds of conjugated pi-electron systems act as chromophores and absorb light in the 200 to 800 nm region. These include unsaturated aldehydes and ketones and aromatic ring compounds. A few examples are displayed below. The spectrum of the unsaturated ketone (on the left) illustrates the advantage of a logarithmic display of molar absorptivity. The π ^__> π* absorption located at 242 nm is very strong, with an ε = 18,000. The weak n ^__> π* absorption near 300 nm has an ε = 100.

Benzene exhibits very strong light absorption near 180 nm (ε > 65,000) , weaker absorption at 200 nm (ε = 8,000) and a group of much weaker bands at 254 nm (ε = 240). Only the last group of absorptions are completely displayed because of the 200 nm cut-off characteristic of most spectrophotometers. The added conjugation in naphthalene, anthracene and tetracene causes bathochromic shifts of these absorption bands, as displayed in the chart on the left below. All the absorptions do not shift by the same amount, so for anthracene (green shaded box) and tetracene (blue shaded box) the weak absorption is obscured by stronger bands that have experienced a greater red shift. As might be expected from their spectra, naphthalene and anthracene are colorless, but tetracene is orange.

The spectrum of the bicyclic diene (above right) shows some vibrational fine structure, but in general is similar in appearance to that of isoprene, shown above. Closer inspection discloses that the absorption maximum of the more highly substituted diene has moved to a longer wavelength by about 15 nm. This "substituent effect" is general for dienes and trienes, and is even more pronounced for enone chromophores.

Walden inversion

Walden inversion is the inversion of a chiral center in a molecule in a chemical reaction. Since a molecule can form two enantiomers around a chiral center, the Walden inversion converts the configuration of the molecule from one enantiomeric form to the other. For example, in a S_N2 reaction, Walden inversion occurs at a tetrahedral carbon atom. It can be visualized by imagining an umbrella turned inside-out in a gale.

It was first observed by chemist Paul Walden in 1896. He was able to convert one enantiomer of a chemical compound into the other enantiomer and back again in a so-called Walden cycle which went like this: (+) chlorosuccinic acid (1 in scheme 1) was converted to (+) malic acid 2 by action of silver oxidein water with retention of configuration, in the next step the hydroxyl group was replaced by chlorine to the other isomer of chlorosuccinic acid 3 by reaction with phosphorus pentachloride, a second reaction with silver oxide yielded (-) malic acid 4 and finally a second reaction with PCl returned the cycle to its starting point.

In this reaction the silver oxide in the first step acts as a hydroxide donor and silver does not play an actual role. The intermediates are the carboxyl dianionA which gives an intramolecular nucleophilic substitution to a four-membered β-lactone ring B. The other carboxyl group is also reactive but in silico data show that the transition state for the formation of the three-membered α-lactone is very high. A hydroxyl ion ring-opens the lactone back to the alcohol Cand the net effect of two counts of inversion is retention of configuration.

Forensic Chemistry

Few processes are more important to society than solving crimes, both to protect the public from criminals and to protect the innocent from unjust punishment. Very often, the strength of a prosecution rests on the ability of law enforcement personnel to connect the accused with the victim by matching physical evidence from the crime scene or victim with trace evidence found on or about the person accused of the crime. Forensic investigators consult a wide range of experts who analyze evidence collected at crime scenes and brought to the crime laboratory for examination. Forensic chemists perform specialized analyses to identify materials and learn the nature of such evidence. A highly trained forensic chemist can determine the composition and nature of materials and predict the source as well as matching sample against sample. Modern chemistry employs a wide range of analytical techniques along with traditional methods of analysis.

Physical evidence collected at crime scenes is sealed in special containers to prevent contamination and degradation and is catalogued carefully. A chain of custody is established and documented as the evidence is sent to a forensic laboratory. At the laboratory, the evidence is examined by personnel trained in one of several fields: Forensic serologists examine body fluids, forensic pathologists examine human remains, firearms technicians classify and test firearms and explosives, and forensic chemists determine the composition and identity of materials.

The History of Forensic Chemistry

Poisons were employed by early Egyptians and ancient Greeks and Romans. Democritus was probably the first chemist to study poisons, and he communicated some of his findings to Hippocrates . Poisons were used both for murder and as a means of execution; the philosopher Socrates was condemned to death by drinkinghemlock . Ancient Roman civilization had laws against poisoning in 82 B.C.E. Before the development of systematic, scientific criminal investigation, guilt was determined largely by circumstantial evidence and hearsay. Arsenic was a popular poison in Roman times. It was referred to as inheritance powder in early France. The Blandy trial of 1752 was the first instance of an actual chemical test for poison, and the Marsh test, developed in 1836, was the first reliable analysis that could show scientifically that arsenic was present in the body of a victim.

Every chemist is schooled in general, organic, and analytical chemistry, but forensic chemists also specialize in specific areas of expertise. For example, an inorganic chemist may examine traces of dust by using microchemistry to identify the chemical composition of tiny particles. Another chemist might employ thin-layerchromatography during the analysis of

Forensic scientists examine evidence from crime scenes in an effort to solve crimes. This scientist is removing a piece of blood-stained material gathered at a crime scene for DNA testing.

blood or urine for traces of drugs, and still another might use chemical reactions in test tubes to identify larger samples of compounds.

What Do Forensic Chemists Do?

Forensic chemistry encompasses organic and inorganic analysis, toxicology , arson investigation, and serology . Each method of analysis uses specialized techniques and instrumentation. The process may be as simple as setting up a density gradient column to compare soil samples or as complicated as using a mass spectrometer orneutron activation analysis to characterize an unknown substance.

A wide array of laboratory techniques and instrumentation is used in forensic studies. This includes ultraviolet, infrared, and visible spectrophotometry; neutron activation analysis; gas chromatography and mass spectrophotometry; high pressure liquid chromatography; and atomic absorption spectrophotometry. The techniques and instrumentation chosen depend on the type of sample or substance to be examined.

The fact that most samples examined are not pure substances, but are often mixed with dirt or debris, presents a major challenge to the forensic chemist. This may also be an advantage, as every substance collected at a crime scene is a unique mixture of chemical compounds that can ultimately be identified. Arsonists, for example, often use accelerants such as gasoline or kerosene to speed combustion and spread flames in the interior of a building. A forensic chemist may collect samples of burned and unburned materials, extract the volatile hydrocarbons, and separate the components for analysis by gas chromatography.

Analytical Techniques and Instrumentation

The gas chromatograph (GC) separates volatile substances into separate components by passing the volatile materials through a long absorbent column. The technique is highly reproducible and reliable; since each sample is likely to contain a definite number and type of impurities, it may provide a close match of the unknown accelerant to a known source such as a gasoline tank or hardware store. It may be necessary to vaporize a tiny sample of the material to provide volatile gases for analysis. The components of the vapor are then passed through the column and separated into a number of components, each of which can be captured and analyzed. In most cases, the accelerant will be mixed with portions of burned paint or building materials, making simple identification by examination impossible, but the ability of the GC to separate tiny portions helps in identification.

The GC is often connected to a mass spectrometer. Mass spectrometry (MS) breaks samples apart and separates the ionized fragments by mass and charge. Vast libraries of comparison fragments make computer-aided identification of materials possible even when the sample is very small. Most forensic laboratories have access to a combined gas chromatograph/mass spectrometer (GC/MS). High pressure liquid chromatography (HPLC) separates many types of drugs and may also be combined with MS.

Analysts may use several types of spectrophotometry. A typical spectrophotometer consists of a light source that provides light of a known wavelength; a holder to position solid, liquid, or gaseous samples; and a system of lenses and photocells that compare light shining on the sample with light passing through. A decrease in the intensity of light passing through the substance indicates the presence of materials that absorb light at that wavelength; the absorbance is quantitative and a measure of the concentration of material, and the wavelengths of maximum absorbance are characteristic of the type of material. Infrared spectrophotometry is especially useful for the identification of organic compounds, as bonds between certain atoms readily absorb infrared radiation (IR).

Ultraviolet (UV) spectrophotometry helps distinguish between samples of proteins and nucleic acids such as deoxyribonucleic acid ( DNA ). Atomic

At the Colorado Bureau of Investigation in Boulder, lab agent Kathy Dressel works on DNA evidence in the JonBenet Ramsey murder investigation.

absorption spectrophotometry provides ways of determining absorption and emission spectra, useful tools in the analysis of metals such as bullet fragments.

Nuclear magnetic resonance spectrophotometry (NMR) makes use of the fact that nuclei of some molecules absorb radio frequency radiation in strong magnetic fields. Nuclei in certain molecules absorb radiation at characteristic frequencies, making the identification of even tiny or impure samples possible. X-ray analysis allows the forensic investigator to visualize foreign objects within the body.

In neutron activation analysis, a beam of neutrons from a nuclear reactor is directed at a sample of test material. The material becomes temporarily radioactive, emitting γ -rays that are characteristic of the composition; analysis of the γ -radiation provides a highly accurate and reproducible determination of the content of the sample. This technique has made possible the determination of arsenic in the hair of corpses buried for hundreds of years. In one case, the body of an Arctic explorer who had died under suspicious circumstances during the 1870s was found buried in a coffin surrounded by ice. Neutron activation analysis of hair from the body showed that hair that was several centimeters long contained little arsenic, but that shorter hair closer to the scalp (which had grown in the few days before death) contained high levels of arsenic, indicating that death was probably caused by arsenic poisoning.

Often, the presence of very small impurities makes comparison possible. For example, cars are painted with paints prepared to certain specifications of color and composition, and pigments and binders used vary from one manufacturer to another and even between models from the same distributor. A small sample of paint left at the scene of an accident may be checked for color by spectrophotometry and then analyzed for composition. Perpetrators of many hit-and-run crimes have been convicted on the basis of combined GC/MS analysis of paint chips.

Residues left by burning powder from firearms consist of patterns of particles that have both characteristic physical and chemical properties. Burned powder, for example, usually contains traces of nitrites that yield chemical reactions and traces of metals such as barium that are often present in primers. Both chemical reactions and microscopic analysis (including electron microscopy) are employed in the identification of powder residues on clothes and skin. An early method for detecting gunshot residue on the hands of suspects involved coating the hand with melted paraffin , allowing the paraffin to cool, and then stripping it off. Gunshot residues transferred from skin to paraffin turned blue or green in the presence of diphenylamine, but many common substances such as urine gave a false positive test. The Greiss reagent is much more definitive, and additional tests can identify traces of lead around bullet holes. Even microscopic particles are found to have definite compositions and can be unequivocally identified.

Toxicology

Toxicologists examine a wide range of materials such as blood stains, urine, and blood gases for traces of poisons or drugs. Many businesses now require the drug screening of employees; it is the responsibility of the technician to distinguish between the presence of illegal drugs and metabolites from foods such as poppy seeds. Such tests may be as simple as paper or thin-layer chromatography or as complicated as gas chromatographic or electrophoretic and serological analysis of a blood sample. Following death by unknown cause, samples of the victim's lungs, blood, urine, vitreous humor, and stomach contents are examined for traces of poisons or medication. Insects found on or near corpses are also collected and examined; they may actually absorb traces of drugs or poisons from the body, and in fact, traces of poisons sometimes are found in the surrounding insects long after concentrations in the body have fallen below detectable limits.

Forensic biochemists perform blood typing and enzyme tests on body fluids in cases involving assault, and also in paternity cases. Even tiny samples of blood, saliva, or semen may be separated by electrophoresis and subjected to enzymatic analysis. In the case of rape, traces of semen found on clothing or on the person become important evidence; the composition of semen varies from person to person. Some individuals excrete enzymes such as acid phosphatase and other proteins that are seldom found outside seminal fluid, and these chemical substances are characteristic of their semen samples. The presence of semen may be shown by the microscopic analysis for the presence of spermatozoa or by a positive test for prostate specific antigen.

In cases of sexual assault, tiny samples of DNA in blood, semen, skin, or hair found on the victim may be purified and the amount of DNA increased by the use of a polymerase chain reaction to produce quantities large enough to analyze. Since DNA is as specific to a person as fingerprints, matching the DNA of a perpetrator to a sample found on a victim is considered to be proof of contact. The Federal Bureau of Investigation (FBI) is currently in the process of establishing a national Combined DNA Index System (CODIS) that will collect data from many states and law enforcement agencies and index it so that particular DNA patterns from evidence collected at many crime scenes can be compared and matched. Many perpetrators of crimes have been convicted and many innocent persons set free after years in prison as a result of DNA analysis.

Testing for Alcohol

Accidents caused by intoxicated drivers kill nearly 15,000 persons a year in the United States alone (almost half of fatal auto accidents are alcohol-related), so a Breathalyzer kit is standard equipment in most police squad cars or state patrol vehicles. Breathalyzers are used to estimate the blood alcohol content of drivers suspected of being intoxicated; the driver may appear sober, but still have a blood alcohol level above the legal limit. Although it is impractical to take blood samples on the highway, research has shown that the concentration of ethanol in the breath bears a definite relationship to its concentration in blood. Many communities have now set a legal limit of 0.08 percent (meaning that 100 milliliters [3.38 fluid ounces] of blood would contain 0.08 grams [0.0028 ounces] of ethanol). In fact, authorities now consider that a person's driving ability is probably impaired at a blood ethanol level of 0.05 percent.

Several types of analytic devices are available to administer Breathalyzer tests. One test makes use of a portable infrared spectrophotometer, another uses a fuel cell, and the most common test employs several glass or plastic tubes and some common chemical reagents. The person being tested blows through a tube, which bubbles the breath through a solution of chemicals containing sulfuric acid, potassium dichromate, water, and silver nitrate. Oxidation of the alcohol results in the reduction of dichromate ion to chromic ion, with a corresponding change in color from orange to green. An electrical device employing a photocell compares the color of the test solution with a standard solution, giving a quantitative determination of the alcohol content. The test provides a quick and reproducible determination of the amount of alcohol in a person's breath and is a numerical measure of the amount of alcohol in the bloodstream. Use of a chemical test helps to avoid subjective opinions of sobriety and provides reliable evidence for court proceedings. The test can be readily and quickly administered by trained law enforcement personnel, but forensic chemists test and calibrate the equipment and testify to its accuracy.

Fingerprinting

Fingerprints on smooth surfaces can often be made visible by the application of light or dark powder, but fingerprints on checks or other documents are often occult (hidden). Occult fingerprints are sometimes made visible by the use of ninhydrin, which turns purple due to reaction with amino acids present in perspiration. Fingerprints or other marks are also sometimes made visible by exposure to high-powered laser light. Some fingerprints can be treated with chemical substances, resulting in a pattern that fluoresces when exposed to light from lasers. Cyanoacrylate ester fumes from glue are used with fluorescent dyes to make the fingerprints visible.

Forensic chemists are usually employed by laboratories in law enforcement agencies or by private testing laboratories and are often called on to provide testimony in court proceedings as expert witnesses. In these cases, the chemist may compare evidence in the case in question to a large number of similar cases he or she has examined and is often asked to give an expert opinion as to the quality of the evidence. Since forensic chemists usually have both a bachelor's degree in chemistry and an advanced degree in forensic science, their academic credentials, along with years of experience and the ability to compare the case in question with a large number of other cases, renders the testimony both valuable and believable.

SN1 reaction

The S_N1 reaction is a substitution reaction in organic chemistry. "S_N" stands for nucleophilic substitution and the "1" represents the fact that the rate-determining step is unimolecular. Thus, the rate equation is often shown as having first-order dependence on electrophile and zero-order dependence on nucleophile. This relationship holds for situations where the amount of nucleophile is much greater than that of the carbocation intermediate. Instead, the rate equation may be more accurately described using steady-state kinetics. The reaction involves a carbocation intermediate and is commonly seen in reactions of secondary or tertiary alkyl halides under strongly basic conditions or, under strongly acidic conditions, with secondary or tertiary alcohols. With primary alkyl halides, the alternative S_N2 reaction occurs. In inorganic chemistry, the S_N1 reaction is often known as the dissociative mechanism. This dissociation pathway is well-described by the cis effect. A reaction mechanism was first proposed by Christopher Ingold et al. in 1940. This reaction does not take account much on the strength of the nucleophile unlike the S_N2 .

Mechanism:-

An example of a reaction taking place with an S_N1 reaction mechanism is the hydrolysis of tert-butyl bromide with water forming tert-butanol:

This S_N1 reaction takes place in three steps:

• Formation of a tert-butyl carbocation by separation of a leaving group (a bromide anion) from the carbon atom: this step is slow and reversible.

• Nucleophilic attack: the carbocation reacts with the nucleophile. If the nucleophile is a neutral molecule (i.e. a solvent) a third step is required to complete the reaction. When the solvent is water, the intermediate is an oxonium ion. This reaction step is fast.

• Deprotonation: Removal of a proton on the protonated nucleophile by water acting as a base forming the alcohol and a hydronium ion. This reaction step is fast.

Scope:-

The S_N1 mechanism tends to dominate when the central carbon atom is surrounded by bulky groups because such groups sterically hinder the S_N2 reaction. Additionally, bulky substituents on the central carbon increase the rate of carbocation formation because of the relief of steric strain that occurs. The resultant carbocation is also stabilized by both inductive stabilization and hyperconjugation from attached alkyl groups. The Hammond-Leffler postulate suggests that this too will increase the rate of carbocation formation. The S_N1 mechanism therefore dominates in reactions at tertiary alkyl centers and is further observed at secondary alkyl centers in the presence of weak nucleophiles.

An example of a reaction proceeding in a S_N1 fashion is the synthesis of 2,5-dichloro-2,5-dimethylhexane from the corresponding diol with concentrated hydrochloric acid:

As the alpha and beta substitutions increase with respect to leaving groups the reaction is diverted from S_N2 to S_N1.

Stereochemistry:-

The carbocation intermediate formed in the reaction's rate limiting step is an sp² hybridized carbon with trigonal planar molecular geometry. This allows two different avenues for the nucleophilic attack, one on either side of the planar molecule. If neither avenue is preferentially favored, these two avenues occur equally, yielding a racemic mix of enantiomers if the reaction takes place at a stereocenter. This is illustrated below in the S_N1 reaction of S-3-chloro-3-methylhexane with an iodide ion, which yields a racemic mixture of 3-iodo-3-methylhexane:

However, an excess of one stereoisomer can be observed, as the leaving group can remain in proximity to the carbocation intermediate for a short time and block nucleophilic attack. This stands in contrast to the S_N2 mechanism, which is a stereospecific mechanism where stereochemistry is always inverted as the nucleophile comes in from the rear side of the leaving group.

Side Reaction:-

Two common side reactions are elimination reactions and carbocation rearrangement. If the reaction is performed under warm or hot conditions (which favor an increase in entropy), E1 eliminationis likely to predominate, leading to formation of an alkene. At lower temperatures, S_N1 and E1 reactions are competitive reactions and it becomes difficult to favor one over the other. Even if the reaction is performed cold, some alkene may be formed. If an attempt is made to perform an S_N1 reaction using a strongly basic nucleophile such as hydroxide or methoxide ion, the alkene will again be formed, this time via an E2 elimination. This will be especially true if the reaction is heated. Finally, if the carbocation intermediate can rearrange to a more stable carbocation, it will give a product derived from the more stable carbocation rather than the simple substitution product.

SN2 reaction

The S_N2 reaction is a type of reaction mechanism that is common in organic chemistry. In this mechanism, one bond is broken and one bond is formed synchronously, i.e., in one step. S_N2 is a kind of nucleophilic substitution reaction mechanism. Since two reacting species are involved in the slow (rate determining) step, this leads to the term substitution nucleophilic (bi-molecular) or S_N2, the other major kind is S_N1.^[1] Many other more specialized mechanisms describe substitution reactions.

The reaction type is so common that it has other names, e.g. "bimolecular nucleophilic substitution", or, among inorganic chemists, "associative substitution" or "interchange mechanism".

Reaction Mechanism

The reaction most often occurs at an aliphatic sp³ carbon center with an electronegative, stable leaving group attached to it (often denoted X), which is frequently a halide atom. The breaking of the C–X bond and the formation of the new bond (often denoted C–Y or C–Nu) occur simultaneously through atransition state in which the carbon under nucleophilic attack is pentacoordinate, and approximately sp² hybridised. The nucleophile attacks the carbon at 180° to the leaving group, since this provides the best overlap between the nucleophile's lone pair and the C–X σ* antibonding orbital. The leaving group is then pushed off the opposite side and the product is formed.

If the substrate under nucleophilic attack is chiral, this can lead, although not necessarily, to an inversion of stereochemistry called a Walden inversion(the nucleophile attacks the electrophilic carbon center, inverting the tetrahedron, much like an umbrella turning inside out in the wind).

In an example of the S_N2 reaction, the attack of Br⁻ (the nucleophile) on an ethyl chloride (the electrophile) results in ethyl bromide, with chloride ejected as the leaving group.

S_N2 reaction of chloroethane with bromide ion:

S_N2 attack occurs if the backside route of attack is not sterically hindered by substituents on the substrate. Therefore this mechanism usually occurs at an unhindered primary carbon centre. If there is steric crowding on the substrate near the leaving group, such as at a tertiary carbon centre, the substitution will involve an S_N1 rather than an S_N2 mechanism, (an S_N1 would also be more likely in this case because a sufficiently stable carbocation intermediary could be formed).

Factor affecting the rate of reaction

i) Substrate

The substrate plays the most important part in determining the rate of the reaction. This is because the nucleophile attacks from the back of the substrate, thus breaking the carbon-leaving group bond and forming the carbon-nucleophile bond. Therefore, to maximise the rate of the S_N2 reaction, the back of the substrate must be as unhindered as possible. Overall, this means that methyl and primary substrates react the fastest, followed by secondary substrates. Tertiary substrates do not participate in S_N2 reactions, because of steric hindrance. Moreover, compounds like '1-chloro 1-ethene' too do not undergo nucleophillic substitution easily because the carbon to chlorine bond is said to be of partial double bond character, thus is harder to break. Another factor leading to an S_N2 reaction due to substrate involves the stability and ease by which the carbocation is formed after removing the leaving group. This means the more stable the carbocation is after removing the leaving group, the more likely it is an S_N1 reaction will occur instead of an S_N2. Among the stabilization methods to be considered are: resonance stabilization, hyper-conjugative stabilization, inductive effect stabilization, or the formation of an aromatic ring molecule (as in the case of 7-chloro cyclohept-1, 3, 5-triene, as it will form a tropolium carbocation which is aromatic).

ii) Nucleophile

Like the substrate, steric hindrance affects the nucleophile's strength. The methoxide anion, for example, is both a strong base and nucleophile because it is a methyl nucleophile, and is thus very much unhindered. tert-Butoxide, on the other hand, is a strong base, but a poor nucleophile, because of its three methyl groups hindering its approach to the carbon. Nucleophile strength is also affected by charge and electronegativity: nucleophilicity increases with increasing negative charge and decreasing electronegativity. For example, OH^- is a better nucleophile than water, and I^- is a better nucleophile than Br^- (in polar protic solvents). In a polar aprotic solvent, nucleophilicity increases up a column of the periodic table as there is no hydrogen bonding between the solvent and nucleophile; in this case nucleophilicity mirrors basicity. I^- would therefore be a weaker nucleophile than Br^- because it is a weaker base. Verdict - A strong/anionic nucleophile always favours S_N2 manner of nucleophillic substitution.

iii) Solvent

The solvent affects the rate of reaction because solvents may or may not surround a nucleophile, thus hindering or not hindering its approach to the carbon atom. Polar aprotic solvents, like tetrahydrofuran, are better solvents for this reaction than polar protic solvents because polar protic solvents will hydrogen bond to the nucleophile, hindering it from attacking the carbon with the leaving group. A polar aprotic solvent with low dielectric constant or a hindered dipole end will favour S_N2 manner of nucleophillic substitution reaction. Examples: DMSO, DMF, acetone etc. In polar aprotic solvent, nucleophilicity parallels basicity.

iv) Leaving group

The leaving group affects the rate of reaction because the more stable it is, the more likely that it will take the two electrons of its carbon-leaving group bond with it when the nucleophile attacks the carbon. Therefore, the weaker the leaving group is as a conjugate base, and thus the stronger its corresponding acid, the better the leaving group. Examples of good leaving groups are therefore the halides (except fluoride) and tosylate, whereas HO^- and H₂N^- are not.

v) Reaction kinetics

The rate of an S_N2 reaction is second order, as the rate-determining step depends on the nucleophile concentration, [Nu⁻] as well as the concentration of substrate, [RX].

r = k[RX][Nu⁻]

This is a key difference between the S_N1 and S_N2 mechanisms. In the S_N1 reaction the nucleophile attacks after the rate-limiting step is over, whereas in S_N2 the nucleophile forces off the leaving group in the limiting step. In other words, the rate of S_N1 reactions depend only on the concentration of the substrate while the S_N2 reaction rate depends on the concentration of both the substrate and nucleophile. In cases where both mechanisms are possible (for example at a secondary carbon centre), the mechanism depends on solvent, temperature, concentration of the nucleophile or on the leaving group.

S_N2 reactions are generally favored in primary alkyl halides or secondary alkyl halides with an aprotic solvent. They occur at a negligible rate in tertiary alkyl halides due to steric hindrance.

It is important to understand that S_N2 and S_N1 are two extremes of a sliding scale of reactions, it is possible to find many reactions which exhibit both S_N2 and S_N1 character in their mechanisms. For instance, it is possible to get a contact ion pairs formed from an alkyl halide in which the ions are not fully separated. When these undergo substitution the stereochemistry will be inverted (as in S_N2) for many of the reacting molecules but a few may show retention of configuration. Sn2 reactions are more common than Sn1 reactions.